MolNFT v1 · #180099 · protein
Asymmetric mtnf-alpha HTNFR1 complex
7KP7 · Tumor necrosis factor: “Asymmetric mtnf-alpha HTNFR1 complex”. X-ray diffraction, 2 ligands (NAG, SO4), 12 pockets (best druggability 0.75). MolNFT v1 #180099 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KP7
- Type
- protein
- Length
- 856 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor; Tumor necrosis factor receptor superfamily member 1A
- UniProt
- P06804, P19438
- Ligands
- NAG, SO4
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Tumor necrosis factor | protein | 148 | 2% helix, 53% strand | P06804 |
| E | Tumor necrosis factor receptor superfamily member 1A | protein | 141 | 2% helix, 42% strand | P19438 |
| D | Tumor necrosis factor receptor superfamily member 1A | protein | 131 | 2% helix, 44% strand | P19438 |
| F | Tumor necrosis factor receptor superfamily member 1A | protein | 140 | 2% helix, 42% strand | P19438 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains E, A, D, B, C, F
- SO4 · Sulfate ion · ion · 30 copies · chains B, A, C, E, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.75 | 0.83 | 58 | SO4 |
| 2 | 65 | 0.74 | 0.99 | 19 | empty |
| 3 | 327 | 0.65 | 0.80 | 40 | empty |
| 4 | 318 | 0.64 | 0.80 | 40 | SO4 |
| 5 | 276 | 0.62 | 0.80 | 42 | empty |
Interfaces
9 interfaces between chains.
- B–A · 1014 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1011 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1001 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 834 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 820 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 7KP7 · asymmetric mTNF-alpha hTNFR1 complex · the same entry in another collection · chain F against F, TM-score 1.00
- P06804 · AlphaFold monomer V2.0 prediction for tumor necrosis factor (P06804) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P19438 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain D against A, TM-score 0.89
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P06804
- Every structure of UniProt P19438
- Elsewhere: RCSB PDB 7KP7 · PDBe 7KP7 · UniProt P06804 · UniProt P19438
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